The behaviour is just the result of the selected implementation. Steam is not doing anything wrong here and therefore I would not call this a bug. If Steam only knows about the game launcher because that´s what is included in the baseline they sent to Steam it can´t do anything else. In other games DLCs are part of the game baseline as well as soon as you purchase them and are installed in a path which is also known by Steam. Then Steam verifies both the game contents and the DLCs and this problem is not happening.
In this game any content, even the standard game files (scenery, airplanes, etc), is unknown for Steam because content is downloaded by the game launcher and by content manager afterwards. In addition to that the configuration files (the ones installed in AppData\Local\Packages\Microsoft.FlightSimulator_8wekyb3d8bbwe) contain the installation path for all content (at the end of UserCfg.opt) and other files that define what game launcher has already installed, but those files are not existing on a fresh installation because they are created by game launcher upon the first game launch. Therefore Steam can´t restore those files either. This could be done by the Xbox cloud sync feature for instance (the one that restores you game settings and controller settings in that configuration pack) or by the Steam cloud sync as well, because Steam also supports the backup of config files on the cloud in many games.
What Steam does during cloud sync is very similar to what Xbox app does too, and is to ask user if he/she wants to restore a backup of the settings and even savegames from the cloud and imports the content in the Steam game ID folder directly, and that´s defined by a unique set of numbers which is the same for everybody (similar to the MSFS case too). But that folder is not affected by the verification process and therefore does not belong to the game baseline which Steam has to compare with your local files. Maybe MSFS could use the existing Xbox app cloud sync to do the same thing with all config files as well except the Packages and Community folders themselves (to have just a backup in the range of MB instead of GB) and just ask user to confirm the installation path on the first game launch (as it does already when a new patch is released). That would be maybe another possible solution.
They made things too complex in my opinion but there must be a reason behind that I guess.
Cheers